I spent a little time on trying to get the 28Cxxx programmer running on my MacBook Pro (OSX 10.8), but I was never even able to get Java to see the RXTX library. Looks like I'll have to try again :-)
This is what ended up (sort of) working for me:
$ ls -l ~/Library/Java/Extensions
lrwxr-xr-x ...

For what it's worth, I've basically given up on using the Arduino IDE here on Linux. It always struck me as being a piece of junk, and then being generally unable to get it to talk with actual hardware reliably, or in some cases at all? Ugh. I very quickly set up avr-gcc, avrdude, a makefile, and ...

From time to time someone on the forum is sure the new parts they just got are dead.

I should have been clearer.
I suspect it died between me receiving it and now, due to some horrible wiring accidents that may have occurred :)

But - I'll continue reducing it down to writing a single byte with ...

No joy with the EEPROMs.
Attempted writing a 1024 byte block at Arduino startup. Still times out on data polling.
I replaced the data polling with 10ms delay, so that all byte write attempts were made.
It still reads back as 0xFF.

BUT - it works with SRAM.
I only had those two EEPROMs, but I've ...

Did you confirm the /CE, /OE, and /WE signals are working?

Good idea - I had checked the wiring, but not the signals.
However, they're working fine, according to some LEDs and this code:

while (true) {
set_ce(HIGH); delay(500);
set_oe(HIGH); delay(500);
set_we(HIGH); delay(500);
set_ce(LOW ...

Address bus and data bus are looking good now.
Here's a read with the data bus tied to the low-byte of the address bus:

0x0000 00 01 02 03 04 05 06 07 08 09 0A 0B 0C 0D 0E 0F 10 11 12 13 14 15 16 17 18 19 1A 1B 1C 1D 1E 1F
... (continues to FF then loops)

Unfortunately I still get timeouts on ...

Argh!
I pulled out everything except the low-byte shift register, and had a sketch looping set_address_bus(0xFFFF).
Instead of staying on constantly, it slowly and randomly blinked on and off (~50% duty cycle).
Swapped the 575, same problem.
Swapped all the wires. Same problem.
Moved the chip eight ...

Oh, also I noticed I did implement a timeout for byte writes in the Arduino. Was the Java freezing up when using my sketch?

Your Java GUI connected to your sketch fails in a much better way:

sending command.
wrote data from 0x0000 to 0x03FF
Error: Communication timeout
data sent.
wrote 8192 ...

Wait ... mkeller's code seems to (despite the comments) shift the low byte, then the high byte:
https://github.com/mkeller0815/MEEPROMMER/blob/acd7c07f54d4f2081bf4de48d0f9bd3d9db713a9/Arduino/MEEPROMMERfirmware/MEEPROMMERfirmware.ino#L140-L143
I think that's contrary to the 74HC595 wiring at http ...

Writes are the problem; any attempt to Write or Erase lock up the Java client indefinitely.

This is probably because the Arduino is waiting for the write to complete. A timeout would be nice but there isn't one. Because your reads aren't working right, the writes will hang. So figure out why the ...

Thanks for all the awesome work.

I'm hoping for a tip on troubleshooting my breadboard build of this.

The data bus appears to work; I can hardwire a byte and see it repeated infinitely for reads.
The address bus appears to work; I added a serial command to manually set an address, and inspect it ...